How to get indicators similar to 10X reports？

[Liripo]

How to get indicators similar to 10X reports？for example: Reads Mapped to TRB

[mourisl]

We don't have a comprehensive QC report like this for now. It's on our TODO list.

[lishuangshuang0616]

Reads Mapped to Any V(D)j Gene is the ratio of reads obtained by fastq-extractor to the total reads approximately equal?

Is "Reads Mapped to TRA" approximately equal to the sum of the average_coverage values of different immune types in annot.fa, divided by the total sum of average_coverage values, and then multiplied by "Reads Mapped to Any V(D)J Gene"?
@mourisl

[mourisl]

fastq-extractor is a bit aggressive, so it will overestimate the reads mapped to VDJ gene regions. This number includes reads mapped to the C gene. The read used in the assembly might be a more accurate estimation of reads mapped to VDJ genes.

The average_coverage is the sum_(read_length) / 500, so you need the read length information, to convert that into read count.

[yuyuleung]

I am wondering how to accurately estimate the number of reads used to assemble each contig, especially when the input reads have varying lengths.

Thanks.

[mourisl]

There is no directly way to accurately estimate the number. One can be through the consensus weight matrix for each contig in the raw.out or final.out file, maybe the deepest coverage point can infer the number of reads. The other is from the "--outputReadAssignment" option, but the assignment is not necessarily corresponds to the assignment in the assembly step.